Computational prediction of L_{3} EXAFS spectra of gold nanoparticles from classical molecular dynamics simulations

We present a computational approach for the simulation of extended x-ray absorption fine structure (EXAFS) spectra of nanoparticles directly from molecular dynamics simulations without fitting any of the structural parameters of the nanoparticle to experimental data. The calculation consists of two stages. First, a molecular dynamics simulation of the nanoparticle is performed and then the EXAFS spectrum is computed from “snapshots” of structures extracted from the simulation. A probability distribution function approach calculated directly from the molecular dynamics simulations is used to ensure a balanced sampling of photoabsorbing atoms and their surrounding scattering atoms while keeping the number of EXAFS calculations that need to be performed to a manageable level. The average spectrum from all configurations and photoabsorbing atoms is computed as an Au L3-edge EXAFS spectrum with the FEFF 8.4 package, which includes the self-consistent calculation of atomic potentials. We validate and apply this approach in simulations of EXAFS spectra of gold nanoparticles with sizes between 20 and 60 Å. We investigate the effect of size, structural anisotropy, and thermal motion on the gold nanoparticle EXAFS spectra and we find that our simulations closely reproduce the experimentally determined spectra

Localization effects on the structural properties of noble metal nanoparticles

We studied the behavior with temperature of the structural parameters of different gold nanoparticles and of their macrocrystalline counterpart (gold foil) by means of EXAFS spectroscopy using synchrotron radiation. The main developments of the work of this thesis concern the possibility to perform temperature dependent XAS experiments on other Au-nanoparticle samples having a narrower size distribution than those studied in this work in order to mask effects to thermal behavior, connected to the dispersion in size

XAS study of lead speciation in a central Italy calcareous soil

""Purpose The Pb absorption processes on a heavy textured calcareous soil, typical of central Italy, were studied using synchrotron X-ray absorption spectroscopy (XAS) in order to probe, at molecular scale, the structure and chemical nature of Pb in contaminated soils and achieve precise description of Pb ions localization into these contaminated soils.. Materials and methods In order to distinguish the role of the different components of soils in Pb retention, samples were prepared from the original soils removing the carbonate fractions, the organic matter, the metal oxides, or selecting the clay fractions. Then these samples were fortified with Pb simulating the natural interactions processes of heavy metal solutions with soils. The quantitative analysis of near edge (XANES) as well extended (EXAFS) regions of Pb LIII edge absorption spectra, in comparison with Pb XAS data of selected reference compounds, allowed the precise determination of local structure and chemical environment of Pb ions in these soil samples.. Results Four components were individuated as the major responsible of Pb retention in calcareous soils: the carbonates, the metal oxide surfaces, the organic matter, and the colloidal inorganic surfaces containing clay components. The structural analysis suggests that, within these experimental conditions, the Pb adsorbed on the soil is generally present as Pb hydroxide with poor crystallization degree. However, the presence of carbonates (CaCO3) induces the co-precipitation of PbCO3-like phases with some degree of crystallinity.. "

Ligands involved in Pb immobilization and transport in lettuce, radish, tomato and Italian ryegrass

Lead (Pb) and other heavy metals represent a great source of concern in agriculture because they may disperse from polluted sources and accumulate in crop organs. This research study was performed with three edible crops and one pasture species (lettuce: Lactuca sativa L. cv. Romana; radish: Raphanus sativus L. var. radicicola; tomato: Lycopersicon lycopersicum L. Karst.; Italian ryegrass: Lolium multiflorum Lam). It was aimed at (1) assessing how species affect Pb distribution among plant organs, (2) determining the extent to which Pb is localized in edible organs, and (3) ascertaining whether it could be possible to distinguish which compounds are responsible for the transport of Pb from one plant organ to another and which compounds are responsible for the accumulation of this metal inside each plant organ. The experiment was conducted in the greenhouse. Plants were grown in plastic pots using a Pb-spiked sandy soil as substrate. Total Pb concentrations in different plant organs and in soil were determined. Within plants, the maximum accumulation of Pb was found in roots while the remaining part of Pb was mainly located in leaves. Pb L-III edge XANES (X-ray Absorption Near Edge Spectroscopy) was applied to identify the principal Pb carrier molecules in the different plant organs. The data suggest that in roots Pb immobilization is mainly due to the complexing ability of histidine, which binds the metal and, to a lesser extent, to precipitation of Pb as carbonate. The transport to the upper plant organs is mainly attributed to Pb complexes with organic acids. In stems and leaves, Pb bonding is mainly carboxylic and amino acid-like, thus confirming the role of these substances in promoting Pb mobility. Thio amino acidic (glutathione and cysteine-like) Pb complexes, which in this study were only found in stems, can also be held responsible for Pb long-distance transport from roots to shoots